Descriptions

Nematodes within the Xiphinema americanum species complex are economically important because they vector
nepoviruses which cause considerable damage to a variety of agricultural crops. The taxonomy of X. americanum species
complex is controversial, with the number of putative species being the subject of debate. Accurate phylogenetic
knowledge of this group is highly desirable as it may ultimately reveal genetic differences between species. For this study,
nematodes belonging to the X. americanum species complex, including potentially mixed species populations, were
collected from 12 geographically disparate locations across the U.S. from different crops and in varying association with
nepoviruses. At least four individuals from each population were analyzed. A portion of the 18S nuclear ribosomal DNA
(rDNA) gene was sequenced for all individuals while the internal transcribed spacer region 1 (ITS1) of rDNA was cloned and
2 to 6 clones per individual were sequenced. Mitochondrial genomes for numerous individuals were sequenced in parallel
using high-throughput DNA sequencing (HTS) technology. Phylogenetic analysis of the 18S rDNA revealed virtually identical
sequences across all populations. Analysis of ITS1 rDNA sequences revealed several well-supported clades, with some
degree of congruence with geographic location and viral transmission, but also numerous presumably paralogous
sequences that failed to form clades with other sequences from the same population. Analysis of mitochondrial DNA
(mtDNA) indicated the presence of three distinct monophyletic clades of X. americanum species complex nematodes. Two
clades contained nematodes found in association with nepovirus and the third contained divergent mtDNA sequences from
three nematode populations from the western U.S. where nepovirus was absent. The inherent heterogeneity in ITS1 rDNA
sequence data and lack of informative sites in 18S rDNA analysis suggests that mtDNA may be more useful in sorting out
the taxonomic confusion of the X. americanum species complex.